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QCAT(1) User Commands QCAT(1)

NAME

qcat - demultiplexing Oxford Nanopore reads from FASTQ files

DESCRIPTION

usage: qcat [-h] [-V] [-l LOG] [--quiet] [-f FASTQ] [-b BARCODE_DIR]

[-o OUTPUT] [--min-score MIN_QUAL] [--detect-middle] [-t THREADS] [--min-read-length MIN_LENGTH] [--tsv] [--trim] [-k {Auto,RAB204,RPB004/RLB001,NBD104/NBD114,
RAB204/RAB214,VMK001,NBD103/NBD104,PBC001,PBK004/LWB001,
RAB214,RBK004,PBC096,RBK001,NBD114,DUAL}] [--list-kits] [--guppy | --epi2me | --dual | --simple] [--no-batch] [--filter-barcodes] [--simple-barcodes SIMPLE_BARCODES]

Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files

options:

show this help message and exit
show program's version number and exit
Print debug information
Don't print summary

General settings:

Barcoded read file
If specified, qcat will demultiplex reads to this folder
Output file trimmed reads will be written to (default: stdout).
Minimum barcode score. Barcode calls with a lower score will be discarded. Must be between 0 and 100. (default: 60)
Search for adapters in the whole read
Number of threads. Only works with in guppy mode
Reads short than <min-read-length> after trimming will be discarded.
Prints a tsv file containing barcode information each read to stdout.
Remove adapter and barcode sequences from reads.

VMK001,NBD103/NBD104,PBC001,PBK004/LWB001,RAB214,RBK004,PBC096,
RBK001,NBD114,DUAL} Sequencing kit. Specifying the correct kit will improve sensitivity and specificity and runtime (default: auto)
List all supported kits

Demultiplexing modes:

Use Guppy's demultiplexing algorithm (default: false)
Use EPI2ME's demultiplexing algorithm (default: true)
Use dual barcoding algorithm
Use simple demultiplexing algorithm. Only looks for barcodes, not for adapter sequences. Use only for testing purposes!

EPI2ME options (only valid with --epi2me):

Don't use information from multiple reads for kit detection (default: false)
Filter rare barcode calls when run in batch mode

Simple options (only valid with --simple):

Use 12 (standard) or 96 (extended) barcodes for demultiplexing

November 2022 qcat 1.1.0